It was a serious charge, and if proven was punishable by death. Hamilton had a powerful friend in Queen Mary, who interfered in his behalf, and he and his companions were committed to ward.
Besides retaining the office of abbot at Paisley, Hamilton was appointed Bishop of Dunkeld in 1543-44 by his brother, acting for the Queen, and after the murder of Cardinal Beaton, on 29th May 1546, was raised to the position of Archbishop of St. Andrews and Primate of Scotland. Probably he never returned to Paisley until, in the adversities of his later years, and the monastery being sacked and burnt by the Reformers, he was forced to take refuge at Dumbarton Castle, where he was made prisoner, and afterwards executed at Stirling. The Master of Sempill had been appointed bailie of the monastery, and, at the dissolution, the whole of the church property was handed over to Lord Sempill. The property finally came into the possession of Lord Claud Hamilton, nephew of the archbishop, and the monastic buildings were converted into the "Place of Paisley," the residence of the Abercorn family.
After the archbishop's execution his body was quartered, and afterwards buried, probably in Paisley. Dr. Lees says:—
"There is in the church a tablet, which looks as if it had marked his grave. It has upon it the archbishop's coat of arms, the letters J. H., the initials of his name, and the motto he assumed, and which contrasts strangely with his troubled life and tragic end—'Misericordia et Pax.'"[383]
Amid all that is said against the last archbishop of the old Church of Scotland, and the last abbot of Paisley, it is well to recall that the "Catechisme," which usually passes under his name, from having been printed at his expense at St. Andrews in 1552, exhibits a solitary instance of an attempt on the part of the old Roman Catholic clergy to convey spiritual instruction to the people, and is creditable to Archbishop Hamilton's memory.[384]
Referring to the disposal of the abbey property, Dr. Lees says:—
"The manner in which the Church property was gifted away forms a scandalous episode in the history of Scotland. Men like Claud Hamilton, who never had done anything for their country, became enriched and ennobled through the spoliation. It is vain to picture regretfully what might have been; but any one can see how much better it would have been for Scotland if the whole community, instead of a few unworthy individuals, had got the benefit of the Church's wealth. Those who did get it have in too many instances made a very miserable use of their ill-gotten gain."[385]
Prior to the Reformation the monastery consisted of a church, the cloister and conventual buildings. The church comprised a long aisleless choir, a nave with aisles, a north transept, a south transept, with St. Mirin's Chapel attached to the south of it, and a tower and spire over the crossing.[386]
The choir walls, containing an elegant sedilia and piscina, remain standing to the height of 9 feet, and it is questioned whether the choir was ever finished during the restoration. There is a string-course all round; the building is of fifteenth century work, and occupies the place of an earlier choir, which has been demolished. The wall at the east end of the nave, which separates it from the transept, may have been erected during the restoration of the fifteenth century, with the intention of rendering the nave a complete church until the transept and choir were restored. This seems to have been in progress when the Reformation interrupted the work. The design of the sedilia resembles that at St. Monans, Fife, and adjoining the sedilia is the piscina, the aperture of which is still visible.
The north transept is in ruins, but the north wall, with the remains of a fine traceried window, still exists, as well as a traceried window in the west wall. The south transept is also in ruins, while the tower and spire have disappeared. St. Mirin's Chapel is well preserved, but the openings connecting it with the south transept are built up.